Wheat is considered as staple food source for 40% of the population worldwide. Yet, the yield and quality can be compromised by fungal diseases, which are also responsible for mycotoxins presence at wheat seeds and originating foodstuff. In this context, the tackling of this problem by developing regulatory limits and standards have induced the development of various methods for sampling, extraction, identification and quantification of mycotoxins in food samples. This review addresses the comparison of the technical and cost efficiency of methods for the extraction and qualitative- quantitative analysis of mycotoxins from whole wheat flour. Methods of extraction such as the Solvent Extraction method, the Liquid Liquid Extraction, the Solid Liquid Extraction, the Solid Phase Extraction, the Immuno-Affinity Columns, the QuEChERS, and the use of absorbent nanomaterials such as graphene oxide and multi-walled carbon nanotubes in extraction procedures, are described in principle, technical details are presented, and examples of reported use are given. Methods of mycotoxin analysis such as Immunological Assays (LFIA, ELISA, FPIA), the Sensor-based (Surface Plasmon Resonance Sensor, Piezoelectric Sensors, Electrochemical Sensors, Colorimetric Sensors), and Chromatographic Techniques (TLC, GC, HPLC, HPLC-FLD, LC-MS/MS, UPLC-MS/MS, UHPLC-MS/MS, UFLC-MS/MS) are reviewed. To compare their efficiency, main advantages and disadvantages, the ongoing improvements, as well as the validation parameters (linearity, recovery range, RSDr range, RSDR %, LOQ range, and cut off) are summarized, and pairing of extraction to analysis methods for specific mycotoxins is provided. It was evidenced that none of methods already in use is capable of analyzing all mycotoxin categories at once, because of their chemical characteristics (volatile/non-volatile, co-elution, UV absorption, fluorescence) versus methods restrictions (matrix interferences, cross-reactivity of antibodies, selectivity and reproducibility of data, need for derivatization, etc). Also, depending on the purpose of the analysis (research or screening as part of legal requirements), to date the immunological methods are only suitable for validated matrices, biosensors can be used for routine screening, and that GC-MS and HPLC-based methods fulfill the legal requirements. In conclusion, while the selectivity and accuracy of methods for mycotoxin detection is being improved rapidly (those sensor-based thanks to the use of nanoparticles, nanomaterials, aptasensors, etc., and the chromatographic techniques coupled with mass spectrometry offer a higher selectivity and sensitivity, low detection limits, maintained resolution performance), and the duration of the analysis, the cost, and the need for highly-skilled staff go in favor of rapid methods (immunological and sensors-based), it is the capacity to fulfill legal requirements, which will determine the trend and their future success in the market. [ABSTRACT FROM AUTHOR]